Teyla, Ronon, and McKay gather for lunch and Teyla notes that Woolsey always eats by himself. Teyla invites him over but he says he's busy preparing for an IOA review. Meanwhile, Sheppard is on the mainland with Dr. Kiang, a biologist. She's going on about the planet's biology when they hear a cry: another scientist, Dr. Parrish has found an amazing plant. Kiang would rather stay with the plant and a bored Sheppard heads back to the Jumper. As he goes back, he hears a noise in the woods and someone stuns him from an ambush.
Sheppard wakes up to discover he's been tied up. He starts to cut himself free. Meanwhile, Woolsey runs into Dr. Vanessa Conrad, a recent arrival. As he goes to his quarters, Vanessa seems interested in him but leaves before Woolsey can say anything more.
Sheppard frees himself but discovers someone took his gun. He goes to the Jumper to find that it's been wrecked.
Zelenka returns from a lab and talks to McKay, who is less than thrilled about talking about the food allergies that ended the banquet he was at. Zelenka says he thinks they should scan the ocean for temperature differentials but McKay disagrees. Woolsey is in the Gate room rehearsing his greeting speech when Chinese Ambassador Shen Xiaoyi arrives and he shows her around the station. Zelenka is still trying to convince McKay to do the temperature scans and the skeptical McKay gives his authorization.
Ambassador Shen assures Woolsey that he's being brought back to Earth to chair a committee. Meanwhile, McKay sets up the scan and they find something deep below sea level.
Sheppard is unable to salvage anything but a knife from the Jumper. He spots a soldier in the woods and tries to sneak up on him, but someone comes up behind Sheppard: Kolya. Another Genii knocks Sheppard out from behind.
Woolsey admits that he doesn't want to leave his job unfinished and is reluctant to go. Shen notices that he's made decisions that run contrary to protocol and his judgment has been compromised. Meanwhile, Zelenka has found the device accounting for the anomalies and brought it to the city.
Sheppard wakes up as Kolya tries to locate the two missing scientists. Sheppard wonders how Kolya survived, and the Genii explains that he used Ancient technology. Kolya has located Atlantis from some of the expedition's unworthy contacts, and plans to launch an attack on the city. He needs an IDC code to send a bomb through the city, and starts torturing Sheppard to get it.
Dr. Conrad visits Woolsey in his quarters and invites him to the movies. He admits he's having a hard time and eventually admits he's being recalled. She points out that if the decision was made, they wouldn't have sent Shen on a three-week journey to inform him of their decision. Woolsey meets with Shen and wonders if she expected him to give up. He concludes that she's there to evaluate him but has already judged him. He figures something else is going on and someone in the IOA wants him gone, and is using Shen to pull it off. He asks what she's getting in return and realizes that she'll be taking over command of Atlantis. She warns that she's in control and there's no way he can win.
Kolya continues to beat Sheppard for the IDC code and tells him that it won't do any good. When Sheppard refuses to talk, Kolya orders two men to his position as he moves to the next step.
McKay detects a low-energy signal from the device but can't figure it out. Zelenka admits that McKay is brilliant and will figure it out. McKay is surprised and Zelenka admits that he is brilliant. Inspired, McKay goes to work.
Sheppard asks what Kolya is preparing to do and he explains they're going to repair the Jumper and launch an attack on Atlantis. He knows he needs the Ancient gene to runt he Jumper and draws his sword to cut off Sheppard's hand if he doesn't get the IDC. Sheppard refuses and Koyla cuts off his hand. Afterward he wonders what Sheppard is running away from.
McKay determines that the device is giving off an electromagnetic signal that is blanketing the entire city. Zelenka suggests they analyze the data but McKay can't decipher the relatively simple script. He decides it's a password and tries to decrypt it. He gets into the system and figures out it's a prompt, the feeds the code back into the system to unlock it.
Woolsey goes to his private spot to contemplate, and finds Conrad there. He thanks her for her suggestion and admits he has the satisfaction of dealing with things. She wishes more people could see him as a good man and he asks her to dinner. She says she'll meet with him later. Banks arrives to say that McKay needs Woolsey, unaware that Shen is watching him. McKay explains that the device is an amazing repository of information and it was designed to seed planets with cells that would evolve into a sentient race. McKay suggests they help it to get to its intended destination but warns that accessing the data would damage the biological specimens.
Kolya's men report saying they've initiated the Jumper but when Kolya turns back to Sheppard, he discovers he's escaped. Kolya insists on dealing with Sheppard first. Meanwhile, Woolsey goes to the control room and asks Banks to contact Dr. Conrad and ell her he'll have to break off his date. Banks says that there's no Dr. Conrad on Atlantis.
Sheppard sets a trap to take out three of Kolya's man. Meanwhile, Woolsey tries to confirm Conrad's existence but Banks says that when she approached him earlier, he was alone. Dr. Keller performs a medical scan but as she does so, Dr. Conrad appears but only Woolsey can see her. After some initial confusion with Keller, Woolsey pretends not to see Conrad for Keller's benefit. Conrad says they need to talk in private and Woolsey quickly downplays his symptoms to get out of the infirmary. Keller gives him some pills but Conrad advises him not to take them.
In the lab, McKay is examining the device's radiation reasons when Zelenka returns. McKay is eager to download the data but recognizes the modulated energy wave and realizes there's a problem.
Sheppard continues to eliminate Kolya's men, while Woolsey confronts Conrad, who says she's a physical manifestation of his sexual and romantic desires. She says that the survival of an entire civilization is at stake and Woolsey realizes it's connected to the device. Shen arrives and notes that she saw him talking to himself earlier. Woolsey tries to dismiss her concerns but Shen questions his sanity. She feels that they should download the information and Woolsey tries to deal with her while Conrad tries to stop him from deciding to destroy the biological specimens. Woolsey believes the potential life is worth the sacrifice and Shen points out it's his chance to follow procedure and keep his job.
Kolya manages to attack Sheppard, throwing him off a cliff. Sheppard hangs on to a root by his one remaining hand and Kolya looks down on him from above.
Woolsey refuses to be threatened, and Conrad begs him to preserve her species. McKay arrives to reveal the electromagnetic signal can cause mass hallucinations and Shen insists they download the data and destroy it. Woolsey gets them out and asks Conrad for an explanation.
Kolya tells Sheppard to use his other question and Sheppard discovers that his hand is there. The Genii tells Sheppard he has no intention of letting him die and encourages him to climb up. Sheppard gets back up and draws his gun, and demands to know what's going on. Kolya says that the Sekkari race faced extinction. Conrad provides the same explanation, noting the Sekkari built seed carriers and programmed them to go to different worlds. Each carriers holds a repository that explains the history of the Sekkari. None reached their goal but the one they found survived re-entry but spent 2,000 years on the ocean's bottom. It activated when it detected a jumper, and linked with Woolsey. "Conrad" is the carrier's artificial intelligent, designed to convince him to free the samples. She apologizes but she couldn't risk telling Woolsey the truth in case he made the wrong decision.
"Kolya" explains that he was sent to occupy Sheppard's mind, since he posed the greatest threat as a military office. It notes that Sheppard's mind provides the distraction, and his greatest fears were manifested.
Conrad tells Woolsey that now he has a decision to make.
Sheppard returns to the scientists and orders them back to the base.
Shen receives a secure transmission from Earth, informing her that the rest of the IOA council has decided they're going with someone else but she'll be rewarded by chairing the IOA's environmental initiative. As Shen leaves, she informs Woolsey he won't be going anyway. She gave him a glowing review to ensure he'd remain on as commander, as revenge for the IOA denying her the command position. As she leaves, Banks admits there haven't been any secure transmission from Earth. Conrad, standing nearby, smiles and Woolsey confronts her. She admits she was responsible for the fake communication. Sheppard and McKay arrive with the carrier and Conrad explains that when it reaches its destination, the program will go to sleep until her objective is fulfilled. She apologizes to Sheppard, who can also see her. Conrad reveals her true form to an eager McKay and they wish her luck as they beam the carrier up to the Apollo to deliver it to its destination.
Later, the team is eating and invites Woolsey to join them. He agrees and McKay feels that they didn't bother with him since he wouldn't have been fooled. However, they point out that Zelenka was off-world the entire time. McKay realizes the device used him to find it and he was fooled all the time.